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Kawatomi K, Morita Y, Katakura Y, Takegawa K, Berepiki A, Higuchi Y. Live cell imaging of β-tubulin mRNA reveals spatiotemporal expression dynamics in the filamentous fungus Aspergillus oryzae. Sci Rep 2024; 14:13797. [PMID: 38877139 PMCID: PMC11178776 DOI: 10.1038/s41598-024-64531-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
In filamentous fungi, microtubules are important for polar growth and morphological maintenance and serve as rails for intracellular trafficking. The molecular mechanisms associated with microtubules have been analyzed. However, little is known about when and where tubulin, a component of microtubules, is biosynthesized in multinuclear and multicellular filamentous fungi. In this study, we visualized microtubules based on the enhanced green fluorescence protein (EGFP)-labeled α-tubulin and β-tubulin mRNA tagged by the EGFP-mediated MS2 system in living yellow Koji mold Aspergillus oryzae cells in order to understand the spatiotemporal production mechanism of tubulin. We found that mRNA of btuA, encoding for β-tubulin, localized at dot-like structures through the apical, middle and basal regions of the hyphal cells. In addition, some btuA mRNA dots showed microtubule-dependent motor protein-like dynamics in the cells. Furthermore, it was found that btuA mRNA dots were decreased in the cytoplasm just before mitosis but increased immediately after mitosis, followed by a gradual decrease. In summary, the localization and abundance of β-tubulin mRNA is spatiotemporally regulated in living A. oryzae hyphal cells.
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Affiliation(s)
- Keishu Kawatomi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Yuki Morita
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Yoshinori Katakura
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | | | - Yujiro Higuchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan.
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2
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Morita Y, Takegawa K, Collins BM, Higuchi Y. Polarity-dependent expression and localization of secretory glucoamylase mRNA in filamentous fungal cells. Microbiol Res 2024; 282:127653. [PMID: 38422859 DOI: 10.1016/j.micres.2024.127653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/06/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
In multinuclear and multicellular filamentous fungi little is known about how mRNAs encoding secreted enzymes are transcribed and localized spatiotemporally. To better understand this process we analyzed mRNA encoding GlaA, a glucoamylase secreted in large amounts by the industrial filamentous fungus Aspergillus oryzae, by the MS2 system, in which mRNA can be visualized in living cells. We found that glaA mRNA was significantly transcribed and localized near the hyphal tip and septum, which are the sites of protein secretion, in polarity-dependent expression and localization manners. We also revealed that glaA mRNA exhibits long-range dynamics in the vicinity of the endoplasmic reticulum (ER) in a manner that is dependent on the microtubule motor proteins kinesin-1 and kinesin-3, but independent of early endosomes. Moreover, we elucidated that although glaA mRNA localized to stress granules (SGs) and processing bodies (PBs) under high temperature, glaA mRNA was not seen under ER stress, suggesting that there are different regulatory mechanisms of glaA mRNA by SG and PB under high temperature and ER stress. Collectively, this study uncovers a dynamic regulatory mechanism of mRNA encoding a secretory enzyme in filamentous fungi.
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Affiliation(s)
- Yuki Morita
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Brett M Collins
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yujiro Higuchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
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3
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Hynes T, Fouyssac M, Puaud M, Joshi D, Chernoff C, Stiebahl S, Michaud L, Belin D. Pan-striatal reduction in the expression of the astrocytic dopamine transporter precedes the development of dorsolateral striatum dopamine-dependent incentive heroin seeking habits. Eur J Neurosci 2024; 59:2502-2521. [PMID: 38650303 DOI: 10.1111/ejn.16354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024]
Abstract
The emergence of compulsive drug-seeking habits, a hallmark feature of substance use disorder, has been shown to be predicated on the engagement of dorsolateral striatal control over behaviour. This process involves the dopamine-dependent functional coupling of the anterior dorsolateral striatum (aDLS) with the nucleus accumbens core, but the mechanisms by which this coupling occurs have not been fully elucidated. The striatum is tiled by a syncytium of astrocytes that express the dopamine transporter (DAT), the level of which is altered in individuals with heroin use disorder. Astrocytes are therefore uniquely placed functionally to bridge dopamine-dependent mechanisms across the striatum. Here we tested the hypothesis that exposure to heroin influences the expression of DAT in striatal astrocytes across the striatum before the development of DLS-dependent incentive heroin seeking habits. Using Western-blot, qPCR, and RNAscope™, we measured DAT protein and mRNA levels in whole tissue, culture and in situ astrocytes from striatal territories of rats with a well-established cue-controlled heroin seeking habit and rats trained to respond for heroin or food under continuous reinforcement. Incentive heroin seeking habits were associated with a reduction in DAT protein levels in the anterior aDLS that was preceded by a heroin-induced reduction in DAT mRNA and protein in astrocytes across the striatum. Striatal astrocytes were also shown to be susceptible to direct dopamine- and opioid-induced downregulation of DAT expression. These results suggest that astrocytes may critically regulate the striatal dopaminergic adaptations that lead to the development of incentive heroin seeking habits.
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Affiliation(s)
- Tristan Hynes
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Maxime Fouyssac
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Mickaël Puaud
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Dhaval Joshi
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Chloe Chernoff
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Sonja Stiebahl
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Lola Michaud
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - David Belin
- Department of Psychology, University of Cambridge, Cambridge, UK
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4
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Clifton NE, Lin JQ, Holt CE, O'Donovan MC, Mill J. Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2024; 95:888-895. [PMID: 38103876 DOI: 10.1016/j.biopsych.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity. METHODS We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. RESULTS Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment. CONCLUSIONS Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
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Affiliation(s)
- Nicholas E Clifton
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
| | - Julie Qiaojin Lin
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, King's College London, London, United Kingdom
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Mill
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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5
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Kilfeather P, Khoo JH, Wagner K, Liang H, Caiazza MC, An Y, Zhang X, Chen X, Connor-Robson N, Shang Z, Wade-Martins R. Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease. Cell Rep 2024; 43:113784. [PMID: 38386560 DOI: 10.1016/j.celrep.2024.113784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/14/2023] [Accepted: 01/27/2024] [Indexed: 02/24/2024] Open
Abstract
The brain is spatially organized and contains unique cell types, each performing diverse functions and exhibiting differential susceptibility to neurodegeneration. This is exemplified in Parkinson's disease with the preferential loss of dopaminergic neurons of the substantia nigra pars compacta. Using a Parkinson's transgenic model, we conducted a single-cell spatial transcriptomic and dopaminergic neuron translatomic analysis of young and old mouse brains. Through the high resolving capacity of single-cell spatial transcriptomics, we provide a deep characterization of the expression features of dopaminergic neurons and 27 other cell types within their spatial context, identifying markers of healthy and aging cells, spanning Parkinson's relevant pathways. We integrate gene enrichment and genome-wide association study data to prioritize putative causative genes for disease investigation, identifying CASR as a regulator of dopaminergic calcium handling. These datasets represent the largest public resource for the investigation of spatial gene expression in brain cells in health, aging, and disease.
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Affiliation(s)
- Peter Kilfeather
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Katherina Wagner
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | | | - Maria Claudia Caiazza
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yanru An
- BGI Research, 49276 Riga, Latvia
| | | | | | - Natalie Connor-Robson
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | | | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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6
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Zhang D, Gao Y, Zhu L, Wang Y, Li P. Advances and opportunities in methods to study protein translation - A review. Int J Biol Macromol 2024; 259:129150. [PMID: 38171441 DOI: 10.1016/j.ijbiomac.2023.129150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024]
Abstract
It is generally believed that the regulation of gene expression involves protein translation occurring before RNA transcription. Therefore, it is crucial to investigate protein translation and its regulation. Recent advancements in biological sciences, particularly in the field of omics, have revolutionized protein translation research. These studies not only help characterize changes in protein translation during specific biological or pathological processes but also have significant implications in disease prevention and treatment. In this review, we summarize the latest methods in ribosome-based translation omics. We specifically focus on the application of fluorescence imaging technology and omics technology in studying overall protein translation. Additionally, we analyze the advantages, disadvantages, and application of these experimental methods, aiming to provide valuable insights and references to researchers studying translation.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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7
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van Oostrum M, Blok TM, Giandomenico SL, Tom Dieck S, Tushev G, Fürst N, Langer JD, Schuman EM. The proteomic landscape of synaptic diversity across brain regions and cell types. Cell 2023; 186:5411-5427.e23. [PMID: 37918396 PMCID: PMC10686415 DOI: 10.1016/j.cell.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/18/2023] [Accepted: 09/28/2023] [Indexed: 11/04/2023]
Abstract
Neurons build synaptic contacts using different protein combinations that define the specificity, function, and plasticity potential of synapses; however, the diversity of synaptic proteomes remains largely unexplored. We prepared synaptosomes from 7 different transgenic mouse lines with fluorescently labeled presynaptic terminals. Combining microdissection of 5 different brain regions with fluorescent-activated synaptosome sorting (FASS), we isolated and analyzed the proteomes of 18 different synapse types. We discovered ∼1,800 unique synapse-type-enriched proteins and allocated thousands of proteins to different types of synapses (https://syndive.org/). We identify shared synaptic protein modules and highlight the proteomic hotspots for synapse specialization. We reveal unique and common features of the striatal dopaminergic proteome and discover the proteome signatures that relate to the functional properties of different interneuron classes. This study provides a molecular systems-biology analysis of synapses and a framework to integrate proteomic information for synapse subtypes of interest with cellular or circuit-level experiments.
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Affiliation(s)
- Marc van Oostrum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Thomas M Blok
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | | | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Nicole Fürst
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
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8
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Burkert N, Roy S, Häusler M, Wuttke D, Müller S, Wiemer J, Hollmann H, Oldrati M, Ramirez-Franco J, Benkert J, Fauler M, Duda J, Goaillard JM, Pötschke C, Münchmeyer M, Parlato R, Liss B. Deep learning-based image analysis identifies a DAT-negative subpopulation of dopaminergic neurons in the lateral Substantia nigra. Commun Biol 2023; 6:1146. [PMID: 37950046 PMCID: PMC10638391 DOI: 10.1038/s42003-023-05441-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Here we present a deep learning-based image analysis platform (DLAP), tailored to autonomously quantify cell numbers, and fluorescence signals within cellular compartments, derived from RNAscope or immunohistochemistry. We utilised DLAP to analyse subtypes of tyrosine hydroxylase (TH)-positive dopaminergic midbrain neurons in mouse and human brain-sections. These neurons modulate complex behaviour, and are differentially affected in Parkinson's and other diseases. DLAP allows the analysis of large cell numbers, and facilitates the identification of small cellular subpopulations. Using DLAP, we identified a small subpopulation of TH-positive neurons (~5%), mainly located in the very lateral Substantia nigra (SN), that was immunofluorescence-negative for the plasmalemmal dopamine transporter (DAT), with ~40% smaller cell bodies. These neurons were negative for aldehyde dehydrogenase 1A1, with a lower co-expression rate for dopamine-D2-autoreceptors, but a ~7-fold higher likelihood of calbindin-d28k co-expression (~70%). These results have important implications, as DAT is crucial for dopamine signalling, and is commonly used as a marker for dopaminergic SN neurons.
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Affiliation(s)
- Nicole Burkert
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Shoumik Roy
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany.
| | - Max Häusler
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | | | - Sonja Müller
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Johanna Wiemer
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Helene Hollmann
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Marvin Oldrati
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Jorge Ramirez-Franco
- UMR_S 1072, Aix Marseille Université, INSERM, Faculté de Médecine Secteur Nord, Marseille, France
- INT, Aix Marseille Université, CNRS, Campus Santé Timone, Marseille, France
| | - Julia Benkert
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Michael Fauler
- Institute of General Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Johanna Duda
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Jean-Marc Goaillard
- UMR_S 1072, Aix Marseille Université, INSERM, Faculté de Médecine Secteur Nord, Marseille, France
- INT, Aix Marseille Université, CNRS, Campus Santé Timone, Marseille, France
| | - Christina Pötschke
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Moritz Münchmeyer
- Wolution GmbH & Co. KG, 82152, Munich, Germany
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Rosanna Parlato
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany
- Division of Neurodegenerative Disorders, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, 68167, Mannheim, Germany
| | - Birgit Liss
- Institute of Applied Physiology, Medical Faculty, Ulm University, 89081, Ulm, Germany.
- Linacre College & New College, Oxford University, OX1 2JD, Oxford, UK.
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9
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Yamamoto Y, Takahata K, Kubota M, Takeuchi H, Moriguchi S, Sasaki T, Seki C, Endo H, Matsuoka K, Tagai K, Kimura Y, Kurose S, Mimura M, Kawamura K, Zhang MR, Higuchi M. Association of protein distribution and gene expression revealed by positron emission tomography and postmortem gene expression in the dopaminergic system of the human brain. Eur J Nucl Med Mol Imaging 2023; 50:3928-3936. [PMID: 37581725 DOI: 10.1007/s00259-023-06390-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023]
Abstract
PURPOSE The topological distribution of dopamine-related proteins is determined by gene transcription and subsequent regulations. Recent research strategies integrating positron emission tomography with a transcriptome atlas have opened new opportunities to understand the influence of regulation after transcription on protein distribution. Previous studies have reported that messenger (m)-RNA expression levels spatially correlate with the density maps of serotonin receptors but not with those of transporters. This discrepancy may be due to differences in regulation after transcription between presynaptic and postsynaptic proteins, which have not been studied in the dopaminergic system. Here, we focused on dopamine D1 and D2/D3 receptors and dopamine transporters and investigated their region-wise relationship between mRNA expression and protein distribution. METHODS We examined the region-wise correlation between regional binding potentials of the target region relative to that of non-displaceable tissue (BPND) values of 11C-SCH-23390 and mRNA expression levels of dopamine D1 receptors (D1R); regional BPND values of 11C-FLB-457 and mRNA expression levels of dopamine D2/D3 receptors (D2/D3R); and regional total distribution volume (VT) values of 18F-FE-PE2I and mRNA expression levels of dopamine transporters (DAT) using Spearman's rank correlation. RESULTS We found significant positive correlations between regional BPND values of 11C-SCH-23390 and the mRNA expression levels of D1R (r = 0.769, p = 0.0021). Similar to D1R, regional BPND values of 11C-FLB-457 positively correlated with the mRNA expression levels of D2R (r = 0.809, p = 0.0151) but not with those of D3R (r = 0.413, p = 0.3095). In contrast to D1R and D2R, no significant correlation between VT values of 18F-FE-PE2I and mRNA expression levels of DAT was observed (r = -0.5934, p = 0.140). CONCLUSION We found a region-wise correlation between the mRNA expression levels of dopamine D1 and D2 receptors and their respective protein distributions. However, we found no region-wise correlation between the mRNA expression levels of dopamine transporters and their protein distributions, indicating different regulatory mechanisms for the localization of pre- and postsynaptic proteins. These results provide a broader understanding of the application of the transcriptome atlas to neuroimaging studies of the dopaminergic nervous system.
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Affiliation(s)
- Yasuharu Yamamoto
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Keisuke Takahata
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan.
| | - Manabu Kubota
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
- Department of Psychiatry, Kyoto University Graduate School of Medicine, 54 Shogoin Kawahara-Cho, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Hiroyoshi Takeuchi
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Sho Moriguchi
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
| | - Takeshi Sasaki
- Department of Psychiatry, Tokyo Metropolitan Bokutoh Hospital, 4-23-15 Kotobashi, Sumida-Ku, Tokyo, 130-8575, Japan
| | - Chie Seki
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
| | - Hironobu Endo
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
| | - Kiwamu Matsuoka
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
| | - Kenji Tagai
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
| | - Yasuyuki Kimura
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
- Department of Clinical and Experimental Neuroimaging, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, 7-430 Morioka, Obu, Aichi, 474-8511, Japan
| | - Shin Kurose
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
| | - Masaru Mimura
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Kazunori Kawamura
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, Chiba, 263-8555, Japan
| | - Ming-Rong Zhang
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, Chiba, 263-8555, Japan
| | - Makoto Higuchi
- Department of Functional Brain Imaging, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba, 263-8555, Japan
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10
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Azcorra M, Gaertner Z, Davidson C, He Q, Kim H, Nagappan S, Hayes CK, Ramakrishnan C, Fenno L, Kim YS, Deisseroth K, Longnecker R, Awatramani R, Dombeck DA. Unique functional responses differentially map onto genetic subtypes of dopamine neurons. Nat Neurosci 2023; 26:1762-1774. [PMID: 37537242 PMCID: PMC10545540 DOI: 10.1038/s41593-023-01401-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
Abstract
Dopamine neurons are characterized by their response to unexpected rewards, but they also fire during movement and aversive stimuli. Dopamine neuron diversity has been observed based on molecular expression profiles; however, whether different functions map onto such genetic subtypes remains unclear. In this study, we established that three genetic dopamine neuron subtypes within the substantia nigra pars compacta, characterized by the expression of Slc17a6 (Vglut2), Calb1 and Anxa1, each have a unique set of responses to rewards, aversive stimuli and accelerations and decelerations, and these signaling patterns are highly correlated between somas and axons within subtypes. Remarkably, reward responses were almost entirely absent in the Anxa1+ subtype, which instead displayed acceleration-correlated signaling. Our findings establish a connection between functional and genetic dopamine neuron subtypes and demonstrate that molecular expression patterns can serve as a common framework to dissect dopaminergic functions.
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Affiliation(s)
- Maite Azcorra
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
- Department of Neurology, Northwestern University, Chicago, IL, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Zachary Gaertner
- Department of Neurology, Northwestern University, Chicago, IL, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Connor Davidson
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Qianzi He
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Hailey Kim
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Shivathmihai Nagappan
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Cooper K Hayes
- Department of Microbiology and Immunology, Northwestern University, Chicago, IL, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
| | - Lief Fenno
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Neuroscience & Psychiatry, The University of Texas at Austin, Austin, TX, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard Longnecker
- Department of Microbiology and Immunology, Northwestern University, Chicago, IL, USA
| | - Rajeshwar Awatramani
- Department of Neurology, Northwestern University, Chicago, IL, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Daniel A Dombeck
- Department of Neurobiology, Northwestern University, Evanston, IL, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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11
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Li Y, Lu Y, Kang C, Li P, Chen L. Revealing Tissue Heterogeneity and Spatial Dark Genes from Spatially Resolved Transcriptomics by Multiview Graph Networks. RESEARCH (WASHINGTON, D.C.) 2023; 6:0228. [PMID: 37736108 PMCID: PMC10511271 DOI: 10.34133/research.0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023]
Abstract
Spatially resolved transcriptomics (SRT) is capable of comprehensively characterizing gene expression patterns and providing an unbiased image of spatial composition. To fully understand the organizational complexity and tumor immune escape mechanism, we propose stMGATF, a multiview graph attention fusion model that integrates gene expression, histological images, spatial location, and gene association. To better extract information, stMGATF exploits SimCLRv2 for visual feature exaction and employs edge feature enhanced graph attention networks for the learning potential embedding of each view. A global attention mechanism is used to adaptively integrate 3 views to obtain low-dimensional representation. Applied to diverse SRT datasets, stMGATF is robust and outperforms other methods in detecting spatial domains and denoising data even with different resolutions and platforms. In particular, stMGATF contributes to the elucidation of tissue heterogeneity and extraction of 3-dimensional expression domains. Importantly, considering the associations between genes in tumors, stMGATF can identify the spatial dark genes ignored by traditional methods, which can be used to predict tumor-driving transcription factors and reveal tumor immune escape mechanisms, providing theoretical evidence for the development of new immunotherapeutic strategies.
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Affiliation(s)
- Ying Li
- School of Mathematics and Statistics,
Henan University of Science and Technology, Luoyang, 471023, China
| | - Yuejing Lu
- School of Mathematics and Statistics,
Henan University of Science and Technology, Luoyang, 471023, China
| | - Chen Kang
- School of Mathematics and Statistics,
Henan University of Science and Technology, Luoyang, 471023, China
| | - Peiluan Li
- School of Mathematics and Statistics,
Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, Henan, 471003, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science,
Chinese Academy of Sciences, Shanghai, 201100, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study,
University of Chinese Academy of Sciences, Hangzhou, 310000, China
- School of Life Science and Technology,
ShanghaiTech University, Shanghai, 201100, China
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12
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Hobson BD, Herzog E. Methodological concerns and lack of evidence for single-synapse RNA-seq. Nat Biotechnol 2023; 41:1221-1224. [PMID: 37500915 DOI: 10.1038/s41587-023-01877-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Affiliation(s)
- Benjamin D Hobson
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA.
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Psychiatry, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA.
| | - Etienne Herzog
- University of Bordeaux, CNRS, IINS, UMR 5297, Bordeaux, France.
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13
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Ament SA, Poulopoulos A. The brain's dark transcriptome: Sequencing RNA in distal compartments of neurons and glia. Curr Opin Neurobiol 2023; 81:102725. [PMID: 37196598 PMCID: PMC10524153 DOI: 10.1016/j.conb.2023.102725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/22/2023] [Accepted: 04/02/2023] [Indexed: 05/19/2023]
Abstract
Transcriptomic approaches are powerful strategies to map the molecular diversity of cells in the brain. Single-cell genomic atlases have now been compiled for entire mammalian brains. However, complementary techniques are only just beginning to map the subcellular transcriptomes from distal cellular compartments. We review single-cell datasets alongside subtranscriptome data from the mammalian brain to explore the development of cellular and subcellular diversity. We discuss how single-cell RNA-seq misses transcripts localized away from cell bodies, which form the 'dark transcriptome' of the brain: a collection of subtranscriptomes in dendrites, axons, growth cones, synapses, and endfeet with important roles in brain development and function. Recent advances in subcellular transcriptome sequencing are beginning to reveal these elusive pools of RNA. We outline the success stories to date in uncovering the constituent subtranscriptomes of neurons and glia, as well as present the emerging toolkit that is accelerating the pace of subtranscriptome discovery.
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Affiliation(s)
- Seth A Ament
- Department of Psychiatry, UM-MIND, and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alexandros Poulopoulos
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA.
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14
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Hobson BD, Stanley AT, De Los Santos MB, Culbertson B, Mosharov EV, Sims PA, Sulzer D. Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Brain Behav Immun 2023; 111:277-291. [PMID: 37100211 PMCID: PMC10460506 DOI: 10.1016/j.bbi.2023.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 04/28/2023] Open
Abstract
Dysregulated inflammation within the central nervous system (CNS) contributes to neuropathology in infectious, autoimmune, and neurodegenerative disease. With the exception of microglia, major histocompatibility complex (MHC) proteins are virtually undetectable in the mature, healthy central nervous system (CNS). Neurons have generally been considered incapable of antigen presentation, and although interferon gamma (IFN-γ) can elicit neuronal MHC class I (MHC-I) expression and antigen presentation in vitro, it has been unclear whether similar responses occur in vivo. Here we directly injected IFN-γ into the ventral midbrain of mature mice and analyzed gene expression profiles of specific CNS cell types. We found that IFN-γ upregulated MHC-I and associated mRNAs in ventral midbrain microglia, astrocytes, oligodendrocytes, and GABAergic, glutamatergic, and dopaminergic neurons. The core set of IFN-γ-induced genes and their response kinetics were similar in neurons and glia, but with a lower amplitude of expression in neurons. A diverse repertoire of genes was upregulated in glia, particularly microglia, which were the only cells to undergo cellular proliferation and express MHC classII (MHC-II) and associated genes. To determine if neurons respond directly via cell-autonomous IFN-γ receptor (IFNGR) signaling, we produced mutant mice with a deletion of the IFN-γ-binding domain of IFNGR1 in dopaminergic neurons, which resulted in a complete loss of dopaminergic neuronal responses to IFN-γ. Our results demonstrate that IFN-γ induces neuronal IFNGR signaling and upregulation of MHC-I and related genes in vivo, although the expression level is low compared to oligodendrocytes, astrocytes, and microglia.
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Affiliation(s)
- Benjamin D Hobson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Adrien T Stanley
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Mark B De Los Santos
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Bruce Culbertson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Eugene V Mosharov
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, United States; Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
| | - David Sulzer
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Pharmacology, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
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15
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Fang Z, Ford AJ, Hu T, Zhang N, Mantalaris A, Coskun AF. Subcellular spatially resolved gene neighborhood networks in single cells. CELL REPORTS METHODS 2023; 3:100476. [PMID: 37323566 PMCID: PMC10261906 DOI: 10.1016/j.crmeth.2023.100476] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 02/18/2023] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
Image-based spatial omics methods such as fluorescence in situ hybridization (FISH) generate molecular profiles of single cells at single-molecule resolution. Current spatial transcriptomics methods focus on the distribution of single genes. However, the spatial proximity of RNA transcripts can play an important role in cellular function. We demonstrate a spatially resolved gene neighborhood network (spaGNN) pipeline for the analysis of subcellular gene proximity relationships. In spaGNN, machine-learning-based clustering of subcellular spatial transcriptomics data yields subcellular density classes of multiplexed transcript features. The nearest-neighbor analysis produces heterogeneous gene proximity maps in distinct subcellular regions. We illustrate the cell-type-distinguishing capability of spaGNN using multiplexed error-robust FISH data of fibroblast and U2-OS cells and sequential FISH data of mesenchymal stem cells (MSCs), revealing tissue-source-specific MSC transcriptomics and spatial distribution characteristics. Overall, the spaGNN approach expands the spatial features that can be used for cell-type classification tasks.
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Affiliation(s)
- Zhou Fang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Machine Learning Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA
| | - Adam J. Ford
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Thomas Hu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nicholas Zhang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA
| | - Athanasios Mantalaris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Ahmet F. Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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16
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Olsen TR, Talla P, Furnari J, Bruce JN, Canoll P, Zha S, Sims PA. Scalable co-sequencing of RNA and DNA from individual nuclei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527940. [PMID: 36798358 PMCID: PMC9934633 DOI: 10.1101/2023.02.09.527940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution. However, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented, and separated into individual droplets for mRNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits without experimental modification. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from both cell lines and archived surgical specimens for associating gene expression phenotypes with both copy number and single nucleotide variants.
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Affiliation(s)
- Timothy R Olsen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Pranay Talla
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Julia Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032
| | - Jeffrey N Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032
| | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032
| | - Shan Zha
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032
- Institute for Cancer Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
- Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, 10032
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032
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17
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Evans R. Dendritic involvement in inhibition and disinhibition of vulnerable dopaminergic neurons in healthy and pathological conditions. Neurobiol Dis 2022; 172:105815. [PMID: 35820645 PMCID: PMC9851599 DOI: 10.1016/j.nbd.2022.105815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 01/21/2023] Open
Abstract
Dopaminergic neurons in the substantia nigra pars compacta (SNc) differentially degenerate in Parkinson's Disease, with the ventral region degenerating more severely than the dorsal region. Compared with the dorsal neurons, the ventral neurons in the SNc have distinct dendritic morphology, electrophysiological characteristics, and circuit connections with the basal ganglia. These characteristics shape information processing in the ventral SNc and structure the balance of inhibition and disinhibition in the striatonigral circuitry. In this paper, I review foundational studies and recent work comparing the circuitry of the ventral and dorsal SNc neurons and discuss how loss of the ventral neurons early in Parkinson's Disease could affect the overall balance of inhibition and disinhibition of dopamine signals.
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Affiliation(s)
- R.C. Evans
- Georgetown University Medical Center, Department of Neuroscience, United States of America
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18
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Paget-Blanc V, Pfeffer ME, Pronot M, Lapios P, Angelo MF, Walle R, Cordelières FP, Levet F, Claverol S, Lacomme S, Petrel M, Martin C, Pitard V, De Smedt Peyrusse V, Biederer T, Perrais D, Trifilieff P, Herzog E. A synaptomic analysis reveals dopamine hub synapses in the mouse striatum. Nat Commun 2022; 13:3102. [PMID: 35660742 PMCID: PMC9166739 DOI: 10.1038/s41467-022-30776-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Dopamine transmission is involved in reward processing and motor control, and its impairment plays a central role in numerous neurological disorders. Despite its strong pathophysiological relevance, the molecular and structural organization of the dopaminergic synapse remains to be established. Here, we used targeted labelling and fluorescence activated sorting to purify striatal dopaminergic synaptosomes. We provide the proteome of dopaminergic synapses with 57 proteins specifically enriched. Beyond canonical markers of dopamine neurotransmission such as dopamine biosynthetic enzymes and cognate receptors, we validated 6 proteins not previously described as enriched. Moreover, our data reveal the adhesion of dopaminergic synapses to glutamatergic, GABAergic or cholinergic synapses in structures we named “dopamine hub synapses”. At glutamatergic synapses, pre- and postsynaptic markers are significantly increased upon association with dopamine synapses. Dopamine hub synapses may thus support local dopaminergic signalling, complementing volume transmission thought to be the major mechanism by which monoamines modulate network activity. The neurotransmitter dopamine is an important regulator of brain function. Here the authors describe “dopamine hub synapses”, where dopamine transmission may act in synergy with other neurotransmitters.
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Affiliation(s)
- Vincent Paget-Blanc
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Marlene E Pfeffer
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Marie Pronot
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Paul Lapios
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Maria-Florencia Angelo
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Roman Walle
- Univ. Bordeaux, INRAE, Bordeaux INP, NutriNeuro, UMR 1286, F-33000, Bordeaux, France
| | - Fabrice P Cordelières
- Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UAR 3420, US 4, F-33000, Bordeaux, France
| | - Florian Levet
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France.,Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UAR 3420, US 4, F-33000, Bordeaux, France
| | | | - Sabrina Lacomme
- Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UAR 3420, US 4, F-33000, Bordeaux, France
| | - Mélina Petrel
- Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UAR 3420, US 4, F-33000, Bordeaux, France
| | - Christelle Martin
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Vincent Pitard
- UB'FACSility CNRS UMS 3427, INSERM US 005, Univ. Bordeaux, F-33000, Bordeaux, France
| | | | - Thomas Biederer
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA
| | - David Perrais
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Pierre Trifilieff
- Univ. Bordeaux, INRAE, Bordeaux INP, NutriNeuro, UMR 1286, F-33000, Bordeaux, France
| | - Etienne Herzog
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000, Bordeaux, France.
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